Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A14 F1 I2 R1 774 49.2 2112398 96.9% 2046913 118.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,082,038 T→C D42D (GAT→GAC)  loiP → Phe‑Phe periplasmic metalloprotease, OM lipoprotein, low salt‑inducible, Era‑binding heat shock protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,082,0380TC100.0% 195.8 / NA 55D42D (GAT→GAC) loiPPhe‑Phe periplasmic metalloprotease, OM lipoprotein, low salt‑inducible, Era‑binding heat shock protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (29/26);  total (29/26)

GAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGATGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATGCGCTAG  >  NC_000913/3081902‑3082153
                                                                                                                                        |                                                                                                                   
gAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACgc                                                                                                                   >  1:985118/1‑139 (MQ=255)
 aaGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGAcgcg                                                                                                                  <  2:329621/139‑1 (MQ=255)
                     gcgcCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGa                                                                                              >  1:537731/1‑139 (MQ=255)
                          ttATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAgg                                                                                         <  1:717156/139‑1 (MQ=255)
                          ttATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAgg                                                                                         <  1:437791/139‑1 (MQ=255)
                           tATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGc                                                                                        <  2:251809/139‑1 (MQ=255)
                                gTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTc                                                                                   <  1:459386/139‑1 (MQ=255)
                                     aaTGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGgag                                                                              >  1:353095/1‑139 (MQ=255)
                                      aTGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGgaga                                                                             >  1:719571/1‑139 (MQ=255)
                                      aTGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGgaga                                                                             >  2:377631/1‑139 (MQ=255)
                                             tGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAg                                                                      >  2:693457/1‑139 (MQ=255)
                                              ggCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAgg                                                                                         >  1:876134/1‑119 (MQ=255)
                                              ggCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAgg                                                                                         <  2:876134/119‑1 (MQ=255)
                                              ggCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGc                                                                     >  2:959582/1‑139 (MQ=255)
                                                        ctgactgGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGcgacga                                                           >  2:1044762/1‑139 (MQ=255)
                                                           actgGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTg                                                        >  2:314699/1‑139 (MQ=255)
                                                             tgGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTgcg                                                      >  2:274448/1‑139 (MQ=255)
                                                               gTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGc                                                                <  2:394661/127‑1 (MQ=255)
                                                               gTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGc                                                                >  1:394661/1‑127 (MQ=255)
                                                               gTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgcc                                                    >  1:120992/1‑139 (MQ=255)
                                                               gTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgcc                                                    >  1:939732/1‑139 (MQ=255)
                                                                ttGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgcca                                                   >  1:862076/1‑139 (MQ=255)
                                                                   ccAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgccagcc                                                <  1:294808/139‑1 (MQ=255)
                                                                     aGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCa                                                                                           >  1:1055800/1‑94 (MQ=255)
                                                                     aGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCa                                                                                           <  2:1055800/94‑1 (MQ=255)
                                                                     aGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAgg                                                                                         <  1:506119/96‑1 (MQ=255)
                                                                     aGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAgg                                                                                         >  2:506119/1‑96 (MQ=255)
                                                                           tGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGa                                        <  1:274448/139‑1 (MQ=255)
                                                                                  cAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCt                                 <  2:353095/139‑1 (MQ=255)
                                                                                  cAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCt                                 >  1:1051483/1‑139 (MQ=255)
                                                                                     cGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAg                                                                                                 <  1:11614/72‑1 (MQ=255)
                                                                                     cGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAg                                                                                                 >  2:11614/1‑72 (MQ=255)
                                                                                      ggACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAAc                             <  2:480156/139‑1 (MQ=255)
                                                                                          tGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCt                         <  1:468677/139‑1 (MQ=255)
                                                                                           gCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCACGGCGAGGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTg                        <  1:705510/139‑1 (MQ=255)
                                                                                            ctctCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGc                                                                                        <  2:573932/74‑1 (MQ=255)
                                                                                            ctctCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGc                                                                                        >  1:573932/1‑74 (MQ=255)
                                                                                            ctctCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGAt                                                          <  2:816403/104‑1 (MQ=255)
                                                                                            ctctCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGAt                                                          >  1:816403/1‑104 (MQ=255)
                                                                                            ctctCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGa                       <  2:985118/139‑1 (MQ=255)
                                                                                            ctctCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGa                       <  2:874375/139‑1 (MQ=255)
                                                                                            ctctCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGa                       >  2:430909/1‑139 (MQ=255)
                                                                                                   caGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTAt                <  1:696208/139‑1 (MQ=255)
                                                                                                      gAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGaa                                                                                                          <  1:638397/46‑1 (MQ=255)
                                                                                                      gAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGaa                                                                                                          >  2:638397/1‑46 (MQ=255)
                                                                                                      gAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGc             >  2:73383/1‑139 (MQ=255)
                                                                                                        gCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCa           <  2:120992/139‑1 (MQ=255)
                                                                                                         cGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAgg                                                                                         >  1:74658/1‑60 (MQ=255)
                                                                                                         cGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAgg                                                                                         <  2:74658/60‑1 (MQ=255)
                                                                                                         cGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCaa          >  1:1046430/1‑139 (MQ=255)
                                                                                                           gAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGa                                                                                                           >  1:233461/1‑40 (MQ=255)
                                                                                                           gAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGa                                                                                                           <  2:233461/40‑1 (MQ=255)
                                                                                                           gAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGc                                                                                        >  1:909290/1‑59 (MQ=255)
                                                                                                           gAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGc                                                                                        <  2:909290/59‑1 (MQ=255)
                                                                                                           gAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATg        >  1:215827/1‑139 (MQ=255)
                                                                                                                 tttCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATGCGCTAg  <  2:1046430/139‑1 (MQ=255)
                                                                                                                                        |                                                                                                                   
GAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGATGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATGCGCTAG  >  NC_000913/3081902‑3082153

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A